Use API to create genes

backend/metagenedb/common/utils/api/baseapi.py

@@ -9,9 +9,9 @@ _LOGGER = logging.getLogger(__name__)
 class LoggedSession(requests.Session):
 
     def request(self, method, url, **kwargs):
-        _LOGGER.info(f"{method.upper()} {url}")
+        _LOGGER.debug(f"{method.upper()} {url}")
         response = super().request(method, url, **kwargs)
-        _LOGGER.info(f"STATUS CODE: {response.status_code}")
+        _LOGGER.debug(f"STATUS CODE: {response.status_code}")
         return response
 
 

backend/scripts/populate_db/import_igc_data.py

@@ -74,6 +74,7 @@ class ImportIGCGenes(object):
         self.skip_functions = skip_functions
 
     def _clean_gene(self, gene_dict):
+        gene_dict['gene_name'] = gene_dict['gene_id']
         gene_dict['gene_id'] = slugify(gene_dict['gene_id'])
         if self.skip_tax:
             gene_dict.pop('taxonomy')
@@ -85,7 +86,7 @@ class ImportIGCGenes(object):
         clean_gene_dict = self._clean_gene(gene_dict)
         try:
             gene_id = clean_gene_dict['gene_id']
-            self.metagenedb_gene_api.get(gene_id)  # Try to get obj to check if it exists
+            gene_obj = self.metagenedb_gene_api.get(gene_id)  # Try to get obj to check if it exists
             self.metagenedb_gene_api.put(gene_id, clean_gene_dict)
         except HTTPError:
             self.metagenedb_gene_api.post(clean_gene_dict)
@@ -96,8 +97,8 @@ class ImportIGCGenes(object):
             gene_dict_with_taxo = select_taxonomy(gene_dict)
             try:
                 self._upsert_gene(gene_dict_with_taxo)
-            except ValidationError as e:
-                _LOGGER.warning(f"{e.__dict__} for gene_id: {gene_dict.get('gene_id')}. Insertion skipped.")
+            except HTTPError as e:
+                _LOGGER.warning(f"{e.response.json()} for gene_id: {gene_dict.get('gene_id')}. Insertion skipped.")
 
     def load_annotation_file_to_db_in_chunks(self, chunk_size=100000):
         processed_genes = 0
@@ -119,7 +120,7 @@ def parse_arguments():
     parser = argparse.ArgumentParser(description='Populate database from a given IGC annotation file.')
     # Common arguments for analysis and annotations
     parser.add_argument('annotation', help='IGC annotation file')
-    parser.add_argument('url', help='base URL of the instance.', default='http://localhost/')
+    parser.add_argument('--url', help='base URL of the instance.', default='http://localhost/')
     parser.add_argument('--skip_taxonomy', action='store_true', help='Skip taxonomy information from genes.')
     parser.add_argument('--skip_functions', action='store_true', help='Skip functions information from genes.')
 
@@ -131,7 +132,9 @@ def parse_arguments():
 
 def run():
     args = parse_arguments()
-    load_annotation_file_to_db_in_chunks(args.annotation, args.url)
+    import_igc_genes = ImportIGCGenes(args.annotation, args.url,
+                                      skip_tax=args.skip_taxonomy, skip_functions=args.skip_functions)
+    import_igc_genes.load_annotation_file_to_db_in_chunks()
 
 
 if __name__ == "__main__":

backend/scripts/populate_db/test_import_igc_data.py

@@ -141,6 +141,40 @@ class TestUpsertGene(APITestCase):
         self.assertEqual(self.api_mock.get('test-gene01')['length'], 356)
 
 
+class TestCleanGene(TestCase):
+
+    def setUp(self):
+        self.import_igc_genes = ImportIGCGenes('test', 'test')
+        self.gene_dict = {
+            'gene_id': 'gene.01',
+            'length': 135,
+            'taxonomy': 'Taxo',
+            'kegg_ko': 'Genus'
+        }
+
+    def test_clean_gene(self):
+        expected_gene_dict = {
+            'gene_id': 'gene-01',
+            'gene_name': 'gene.01',
+            'length': 135,
+            'taxonomy': 'Taxo',
+            'kegg_ko': 'Genus'
+        }
+        test_gene_dict = self.import_igc_genes._clean_gene(self.gene_dict)
+        self.assertDictEqual(test_gene_dict, expected_gene_dict)
+
+    def test_clean_gene_skip_taxo(self):
+        self.import_igc_genes.skip_tax = True
+        expected_gene_dict = {
+            'gene_id': 'gene-01',
+            'gene_name': 'gene.01',
+            'length': 135,
+            'kegg_ko': 'Genus'
+        }
+        test_gene_dict = self.import_igc_genes._clean_gene(self.gene_dict)
+        self.assertDictEqual(test_gene_dict, expected_gene_dict)
+
+
 @pytest.mark.django_db
 class TestSelectTaxonomy(TestCase):